MolNFT v1 · #174086 · protein
Formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex from methanospirillum hungatei (heterodislfide reductase core and mobile arm in conformational state 1, composite structure)
7BKD · Cob--com heterodisulfide reductase iron-sulfur subunit a: “Formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex from…”. Electron microscopy, 4 ligands (SF4, 9S8, FAD), 20 pockets (best…
- PDB
- 7BKD
- Type
- protein
- Length
- 3,177 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cob--com heterodisulfide reductase iron-sulfur subunit a; Cob--com heterodisulfide…
- EC
- 1.8.-.-, 1.2.99.-, 1.17.1.9
- UniProt
- Q2FKZ1, Q2FKZ3, Q2FKZ2, Q2FKZ0, Q2FME3, Q2FRK1
- Ligands
- SF4, 9S8, FAD, FES
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 7 distinct chains · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cob--com heterodisulfide reductase iron-sulfur subunit a (EC 1.8.-.-) | protein | 664 | 28% helix, 23% strand | Q2FKZ1 |
| C, c | Cob--com heterodisulfide reductase subunit C | protein | 189 | 54% helix, 1% strand | Q2FKZ3 |
| B, b | Cob--com heterodisulfide reductase subunit B | protein | 296 | 50% helix, 11% strand | Q2FKZ2 |
| a | Cob--com heterodisulfide reductase iron-sulfur subunit a (EC 1.8.-.-) | protein | 446 | 24% helix, 25% strand | Q2FKZ1 |
| F | F420-non-reducing hydrogenase subunit D | protein | 137 | 46% helix, 15% strand | Q2FKZ0 |
| E | Formate dehydrogenase, beta subunit (F420) (EC 1.2.99.-) | protein | 411 | 43% helix, 16% strand | Q2FME3 |
| D | Formate dehydrogenase (EC 1.17.1.9) | protein | 549 | 35% helix, 14% strand | Q2FRK1 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 18 copies · chains A, a, E, C, c, D
- 9S8 · Non-cubane [4Fe-4S]-cluster · ligand · 4 copies · chains C, B, c, b
- FAD · Flavin-adenine dinucleotide · ligand · 3 copies · chains A, a, E
- FES · Fe2/s2 (inorganic) cluster · ligand · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 527 | 0.81 | 0.87 | 78 | empty |
| 2 | 494 | 0.81 | 0.88 | 59 | FAD |
| 3 | 582 | 0.81 | 0.86 | 74 | FAD |
| 4 | 560 | 0.80 | 0.86 | 77 | FAD |
| 5 | 83 | 0.75 | 0.98 | 18 | empty |
Interfaces
18 interfaces between chains.
- A–a · 3061 Ų buried · 41 hydrogen bonds · protein-protein
- C–B · 2761 Ų buried · 31 hydrogen bonds · protein-protein
- c–b · 2743 Ų buried · 33 hydrogen bonds · protein-protein
- A–F · 2038 Ų buried · 19 hydrogen bonds · protein-protein
- F–E · 2026 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7BKD · Formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q2FKZ1
- Every structure of UniProt Q2FKZ3
- Every structure of UniProt Q2FKZ2
- Every structure of UniProt Q2FKZ0
- Every structure of UniProt Q2FME3
- Every structure of UniProt Q2FRK1
- Elsewhere: RCSB PDB 7BKD · PDBe 7BKD · UniProt Q2FKZ1 · UniProt Q2FKZ3 · UniProt Q2FKZ2 · UniProt Q2FKZ0 · UniProt Q2FME3 · UniProt Q2FRK1
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